Bug#844135: scilab-plotlib: FTBFS: segmentation fault

Lucas Nussbaum lucas at debian.org
Sat Nov 12 20:10:32 UTC 2016 

Source: scilab-plotlib
Version: 0.42-1
Severity: serious
Tags: stretch sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20161111 qa-ftbfs
Justification: FTBFS on amd64

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64.

Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> CDBS WARNING:    simple-patchsys.mk is deprecated since 0.4.85 - please use source format 3.0 (quilt) instead
> make[1]: 'update-config' is up to date.
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> SCI_DISABLE_TK=1 SCI_JAVA_ENABLE_HEADLESS=1 DOCBOOK_ROOT=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh \
> 	/usr/bin/scilab -nw -f builder.sce
> Error: Impossible to define SCIHOME environment variable.
> libEGL warning: DRI3: xcb_connect failed
> libEGL warning: DRI2: xcb_connect failed
> libEGL warning: DRI2: xcb_connect failed
> Caught handled GLException: EGLGLXDrawableFactory - Could not initialize shared resources for EGLGraphicsDevice[type .egl, v0.0.0, connection nil, unitID 0, handle 0x0, owner true, ResourceToolkitLock[obj 0x65d9c875, isOwner true, <20db4aaa, 4200fc3f>[count 1, qsz 0, owner <main-SharedResourceRunner>]]] on thread main-SharedResourceRunner
>     [0]: jogamp.opengl.egl.EGLDrawableFactory$SharedResourceImplementation.createSharedResource(EGLDrawableFactory.java:518)
>     [1]: jogamp.opengl.SharedResourceRunner.run(SharedResourceRunner.java:353)
>     [2]: java.lang.Thread.run(Thread.java:745)
> Caused[0] by GLException: Failed to created/initialize EGL display incl. fallback default: native 0x0, error 0x3001/0x3001 on thread main-SharedResourceRunner
>     [0]: jogamp.opengl.egl.EGLDisplayUtil.eglGetDisplayAndInitialize(EGLDisplayUtil.java:297)
>     [1]: jogamp.opengl.egl.EGLDisplayUtil.access$300(EGLDisplayUtil.java:58)
>     [2]: jogamp.opengl.egl.EGLDisplayUtil$1.eglGetAndInitDisplay(EGLDisplayUtil.java:320)
>     [3]: com.jogamp.nativewindow.egl.EGLGraphicsDevice.open(EGLGraphicsDevice.java:125)
>     [4]: jogamp.opengl.egl.EGLDrawableFactory$SharedResourceImplementation.createEGLSharedResourceImpl(EGLDrawableFactory.java:532)
>     [5]: jogamp.opengl.egl.EGLDrawableFactory$SharedResourceImplementation.createSharedResource(EGLDrawableFactory.java:516)
>     [6]: jogamp.opengl.SharedResourceRunner.run(SharedResourceRunner.java:353)
>     [7]: java.lang.Thread.run(Thread.java:745)
> Building macros...
> -- Creation of [plotliblib] (Macros) --
> genlib: Processing file: %c_i_pltlibH.sci
> genlib: Processing file: %h_i_h.sci
> genlib: Processing file: %pltlibH_c_pltlibH.sci
> genlib: Processing file: %pltlibH_delete.sci
> genlib: Processing file: %pltlibH_e.sci
> genlib: Processing file: %pltlibH_f_pltlibH.sci
> genlib: Processing file: %pltlibH_get.sci
> genlib: Processing file: %pltlibH_p.sci
> genlib: Processing file: %pltlibH_set.sci
> genlib: Processing file: %s_i_pltlibH.sci
> genlib: Processing file: %s_set.sci
> genlib: Processing file: TitleLabel.sci
> genlib: Processing file: _add_event_handler.sci
> genlib: Processing file: _axes.sci
> genlib: Processing file: _axis.sci
> genlib: Processing file: _caxis.sci
> genlib: Processing file: _check2dFun.sci
> genlib: Processing file: _checkTypeAndDimensions.sci
> genlib: Processing file: _cla.sci
> genlib: Processing file: _colorbar.sci
> genlib: Processing file: _colormap.sci
> genlib: Processing file: _compute_data_bounds.sci
> genlib: Processing file: _del_event_handler.sci
> genlib: Processing file: _drawnow.sci
> genlib: Processing file: _error.sci
> genlib: Processing file: _figure.sci
> genlib: Processing file: _fill.sci
> genlib: Processing file: _fill3.sci
> genlib: Processing file: _gca.sci
> genlib: Processing file: _gcf.sci
> genlib: Processing file: _getvalidchildren.sci
> genlib: Processing file: _grid.sci
> genlib: Processing file: _hidden.sci
> genlib: Processing file: _hold.sci
> genlib: Processing file: _image.sci
> genlib: Processing file: _imagesc.sci
> genlib: Processing file: _legend.sci
> genlib: Processing file: _loglog.sci
> genlib: Processing file: _mainPlot.sci
> genlib: Processing file: _mesh.sci
> genlib: Processing file: _parse.sci
> genlib: Processing file: _parse_axes_ppty_value.sci
> genlib: Processing file: _parse_figure_ppty_value.sci
> genlib: Processing file: _parse_leaf_ppty_value.sci
> genlib: Processing file: _parse_property_value.sci
> genlib: Processing file: _pcolor.sci
> genlib: Processing file: _plot.sci
> genlib: Processing file: _plot3.sci
> genlib: Processing file: _plotyy.sci
> genlib: Processing file: _pretty_lims.sci
> genlib: Processing file: _quiver.sci
> genlib: Processing file: _quiver3.sci
> genlib: Processing file: _ratio_one_lims.sci
> genlib: Processing file: _semilogx.sci
> genlib: Processing file: _semilogy.sci
> genlib: Processing file: _shading.sci
> genlib: Processing file: _shg.sci
> genlib: Processing file: _subplot.sci
> genlib: Processing file: _surf.sci
> genlib: Processing file: _surfl.sci
> genlib: Processing file: _toggle.sci
> genlib: Processing file: _trimesh.sci
> genlib: Processing file: _tripcolor.sci
> genlib: Processing file: _triplot.sci
> genlib: Processing file: _trisurf.sci
> genlib: Processing file: _trisurfl.sci
> genlib: Processing file: _uicontrol.sci
> genlib: Processing file: _uimenu.sci
> genlib: Processing file: _update_axes.sci
> genlib: Processing file: _update_figure.sci
> genlib: Processing file: _update_leaf.sci
> genlib: Processing file: _update_shaded_plots.sci
> genlib: Processing file: _update_single_shaded_pl.sci
> genlib: Processing file: _view.sci
> genlib: Processing file: activateRGBColormap.sci
> genlib: Processing file: addPlot.sci
> genlib: Processing file: bluecolormap.sci
> genlib: Processing file: changeVP.sci
> genlib: Processing file: check3dFun.sci
> genlib: Processing file: clf.sci
> genlib: Processing file: computeColor.sci
> genlib: Processing file: computeLight.sci
> genlib: Processing file: coolcolormap.sci
> genlib: Processing file: coppercolormap.sci
> genlib: Processing file: cycleColorsLineStyle.sci
> genlib: Processing file: diffuse.sci
> genlib: Processing file: eval3dPolygons.sci
> genlib: Processing file: findColorIndex.sci
> genlib: Processing file: fliplr.sci
> genlib: Processing file: flipud.sci
> genlib: Processing file: focus.sci
> genlib: Processing file: generate3dPolygons.sci
> genlib: Processing file: generate3dSegments.sci
> genlib: Processing file: getColorNumber.sci
> genlib: Processing file: get_figure_handle.sci
> genlib: Processing file: graphinit.sci
> genlib: Processing file: greencolormap.sci
> genlib: Processing file: lighten.sci
> genlib: Processing file: nonParametricDiffData.sci
> genlib: Processing file: nonParametricDiffDeriv.sci
> genlib: Processing file: nonParametricNormals.sci
> genlib: Processing file: parametricDiffData.sci
> genlib: Processing file: parametricDiffDeriv.sci
> genlib: Processing file: parametricNormals.sci
> genlib: Processing file: parseAxis.sci
> genlib: Processing file: parseAxisLocation.sci
> genlib: Processing file: parseBackFaceCulling.sci
> genlib: Processing file: parseBackFaceLighting.sci
> genlib: Processing file: parseCDataMapping.sci
> genlib: Processing file: parseCaxis.sci
> genlib: Processing file: parseColor.sci
> genlib: Processing file: parseColorBar.sci
> genlib: Processing file: parseColormap.sci
> genlib: Processing file: parseData.sci
> genlib: Processing file: parseDir.sci
> genlib: Processing file: parseGrid.sci
> genlib: Processing file: parseHideMode.sci
> genlib: Processing file: parseLabel.sci
> genlib: Processing file: parseLegend.sci
> genlib: Processing file: parseLight.sci
> genlib: Processing file: parseLim.sci
> genlib: Processing file: parseLineStyle.sci
> genlib: Processing file: parseLineStyleOrder.sci
> genlib: Processing file: parseLineWidth.sci
> genlib: Processing file: parseMargin.sci
> genlib: Processing file: parseMarker.sci
> genlib: Processing file: parseOnOff.sci
> genlib: Processing file: parsePosition.sci
> genlib: Processing file: parseRatio.sci
> genlib: Processing file: parseScale.sci
> genlib: Processing file: parseShading.sci
> genlib: Processing file: parseTicks.sci
> genlib: Processing file: parseView.sci
> genlib: Processing file: plotlib_handler.sci
> genlib: Processing file: plotlib_rotate_handler.sci
> genlib: Processing file: plotlib_subplot_handler.sci
> genlib: Processing file: plotlibmode.sci
> genlib: Processing file: plotlibver.sci
> genlib: Processing file: processColorBar.sci
> genlib: Processing file: processLegend.sci
> genlib: Processing file: redcolormap.sci
> genlib: Processing file: rotate_axes.sci
> genlib: Processing file: scf.sci
> genlib: Processing file: setColors.sci
> genlib: Processing file: setFontSize.sci
> genlib: Processing file: setMarkAndLineProperties.sci
> genlib: Processing file: surfnorm.sci
> genlib: Processing file: whitebg.sci
> genlib: Regenerate names and lib
> Warning : redefining function: uicontrol               . Use funcprot(0) to avoid this message
> 
> Warning : redefining function: uimenu                  . Use funcprot(0) to avoid this message
> 
> Warning: Scilab 6 will not support the file format used.
> Warning: Please quote the variable declaration. Example, save('myData.sod',a) becomes save('myData.sod','a').
> Warning: See help('save') for the rational.
> Warning: Scilab 6 will not support the file format used.
> Warning: Please quote the variable declaration. Example, save('myData.sod',a) becomes save('myData.sod','a').
> Warning: See help('save') for the rational.
> Warning: Scilab 6 will not support the file format used.
> Warning: Please quote the variable declaration. Example, save('myData.sod',a) becomes save('myData.sod','a').
> Warning: See help('save') for the rational.
> Warning: Scilab 6 will not support the file format used.
> Warning: Please quote the variable declaration. Example, save('myData.sod',a) becomes save('myData.sod','a').
> Warning: See help('save') for the rational.
> Warning: Scilab 6 will not support the file format used.
> Warning: Please quote the variable declaration. Example, save('myData.sod',a) becomes save('myData.sod','a').
> Warning: See help('save') for the rational.
> Building help...
> 
> Building the master document:
> 	/<<PKGBUILDDIR>>/help/en_US
> 
> Building the manual file [javaHelp] in /<<PKGBUILDDIR>>/help/en_US.
> Total files without example: 6
> Total generated html files: 43
> Generating loader.sce...
> Generating unloader.sce...
>  
>  
>                                  !--error 42 
> A fatal error has been detected by Scilab.
> Your instance will probably quit unexpectedly soon.
> If a graphic feature has been used, this might be caused by the system graphic drivers.
> Please try to update them and run this feature again.
> You can report a bug on http://bugzilla.scilab.org/ with:
> * a sample code which reproduces the issue
> * the result of [a, b] = getdebuginfo()
> * the following information:
> [ip-172-31-0-73:67980] Signal: Segmentation fault (11)
> [ip-172-31-0-73:67980] Signal code:  (128)
> [ip-172-31-0-73:67980] Failing at address: (nil)
>  
> Call stack:
>    1: 0x8c14a9 <JVM_handle_linux_signal>        (/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/libjvm.so)
>    2: 0x8b5458 < >                              (/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/libjvm.so)
>    3: 0x11100  < >                              (/lib/x86_64-linux-gnu/libpthread.so.0)
>    4: 0x12720  < >                              (/lib/x86_64-linux-gnu/libpthread.so.0)
>    5: 0x35920  < >                              (/lib/x86_64-linux-gnu/libc.so.6)
>    6: 0x3597a  < >                              (/lib/x86_64-linux-gnu/libc.so.6)
>    7: 0x202b8  <__libc_start_main>              (/lib/x86_64-linux-gnu/libc.so.6)
>    8: 0x192a   < >                              (/usr/bin/scilab-bin)
> End of stack
> 
> 
>  
>                                  !--error 999 
> Aborting current computation
>  
> Segmentation fault
> debian/rules:8: recipe for target 'build/scilab-plotlib' failed
> make: *** [build/scilab-plotlib] Error 139

The full build log is available from:
   http://aws-logs.debian.net/2016/11/11/scilab-plotlib_0.42-1_unstable.log

This failure happens on a CPU with TSX extensions available, but is not
reproducible on a machine without them. For context, I recommend reading the
thread starting at https://lists.debian.org/debian-devel/2016/11/msg00210.html

The node used is an Amazon EC2 VM with 64 cores. /proc/cpuinfo says:
   model    : 79
   model name : Intel(R) Xeon(R) CPU E5-2686 v4 @ 2.30GHz
   stepping : 1

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.

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